title: High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants.
abstract: We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events--more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens.
authors.affiliation: Department of Computer Science, North Carolina State University, Raleigh, North Carolina, United States of America.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Howard
authors.forename: Qiwen
authors.initials: Q
authors.lastname: Hu
authors.forename: Ahmet Can
authors.initials: AC
authors.lastname: Babaoglu
authors.forename: Manan
authors.initials: M
authors.lastname: Chandra
authors.forename: Monica
authors.initials: M
authors.lastname: Borghi
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Tan
authors.forename: Luyan
authors.initials: L
authors.lastname: He
authors.forename: Heike
authors.initials: H
authors.lastname: Winter-Sederoff
authors.forename: Walter
authors.initials: W
authors.lastname: Gassmann
authors.forename: Paola
authors.initials: P
authors.lastname: Veronese
authors.forename: Steffen
authors.initials: S
authors.lastname: Heber
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D017360:Arabidopsis / Q000382:microbiology*; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns / Q000235:genetics; D044224:Pseudomonas syringae / Q000235:genetics* / Q000502:physiology*; D022821:RNA Splice Sites / Q000235:genetics; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D022821:RNA Splice Sites